I am been able to send custom data from flight controller, and view it in mavlink inspector. Now i want to obtain and perform my calculations on it. How and where can i access it.
What Mavlink Inspector are you talking about?
Press CTRL-F and select the Mavlink Inspector button.
This helps, get latest Beta or wait for the next release https://github.com/ArduPilot/MissionPlanner/pull/2360